[gmx-users] [Beginner] How can I generate .gro and .top?

David van der Spoel spoel at xray.bmc.uu.se
Thu Jan 18 15:59:54 CET 2007

Marcelo de Freitas Lima wrote:
> Dear all,
> How can I generate a ".gro" and a ".top" from a ".pdb" file of a 
> synthetic polymer residue (548 atoms with a random distribution of 
> monomers)?
> There is some tutorial to use gromacs with strutures like that, instead 
> proteins?
> Problem:
> The PRODRG webserver can't convert my structure, because there is so 
> many atoms.
> Thank you all,
You may want to try x2top, but it will only work for simple molecules.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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